MetNetComp Database [1] / Minimal gene deletions Minimal gene deletions for simulation-based growth-coupled production. You can also see maximal gene deletions.

Model : iML1515 [2].
Target metabolite : trp__L_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (61 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 48
  Gene deletion: b0586 b1241 b0351 b4069 b4384 b2744 b3708 b3614 b0910 b3115 b1849 b2296 b2925 b2097 b2926 b2781 b0030 b2407 b1759 b1982 b2797 b3117 b1814 b4471 b3616 b3589 b3946 b0825 b2440 b4374 b0675 b0261 b0507 b4381 b2406 b0112 b0452 b2975 b0114 b3603 b1539 b2492 b0904 b1533 b3918 b4042 b3662 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.414988 (mmol/gDw/h)
  Minimum Production Rate : 1.166622 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 23.518721
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.965875
  EX_pi_e : 0.400300
  EX_so4_e : 0.104502
  EX_k_e : 0.081003
  EX_mg2_e : 0.003600
  EX_fe2_e : 0.003425
  EX_fe3_e : 0.003240
  EX_ca2_e : 0.002160
  EX_cl_e : 0.002160
  EX_cu2_e : 0.000294
  EX_mn2_e : 0.000287
  EX_zn2_e : 0.000142
  EX_ni2_e : 0.000134
  EX_cobalt2_e : 0.000010

Product: (mmol/gDw/h)
  EX_h2o_e : 45.579275
  EX_co2_e : 24.912562
  EX_h_e : 8.722158
  EX_ac_e : 2.421095
  EX_trp__L_e : 1.166622
  EX_thym_e : 0.075148
  DM_oxam_c : 0.000464
  DM_5drib_c : 0.000278
  EX_dxylnt_e : 0.000278
  DM_4crsol_c : 0.000093
  EX_etha_e : 0.000033

Visualization
  1. Download JSON file.
  2. Go to Escher site [3].
  3. Select "Data > Load reaction data" and apply the downloaded file.

References
[1] Tamura, T. MetNetComp: Database for minimal and maximal gene deletion strategies for growth-coupled production of genome-scale metabolic networks, IEEE/ACM Transactions on Computational Biology and Bioinformatics, in press.
[2] Norsigian, C. J., Pusarla, N., McConn, J. L., Yurkovich, J. T., Dräger, A., Palsson, B. O., & King, Z. (2020). BiGG Models 2020: multi-strain genome-scale models and expansion across the phylogenetic tree. Nucleic acids research, 48(D1), D402-D406.
[3] King, Z. A., Dräger, A., Ebrahim, A., Sonnenschein, N., Lewis, N. E., & Palsson, B. O. (2015). Escher: a web application for building, sharing, and embedding data-rich visualizations of biological pathways. PLoS computational biology, 11(8), e1004321.

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Last updated: 21-Sep-2023
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